The Create Geologic Cross Sections–eXacto Section v. 2.0, ArcMap 9.3 written by Jennifer Carrell of the Illinois State Geological Survey is a handy tool for creating cross sections.
It requires ArcGIS and a 3D Analyst Extension license.
You can create profiles against multiple DEMs at once, define the vertical exaggeration, and have it include contact points. It is well documented and comes with sample data to use with the tutorial.
I did not see it mentioned but it also include a personal geodatabase that include a grid that can be used along with the profiles you create.
If you make profiles, think this is definitely an option you should look at. The fact that it is a VBA application is a bit worrisome in that its lifespan is limited.